[gmx-users] more- mdrun on Beowulf cluster

[David]

On Mon, 2004-01-12 at 21:27, Yu Sun (Denis) wrote:
> I recompile and install the gromacs on my home directory. And type
> mpprun -map 4 mdrun <options...>
> 
> this time it gives error:
>     error while loading shared libraries: libXm.so.1
> 
Sorry about this...
You need to add a configure flag
--without-motif-libraries --without-motif-includes
and maybe as well
--without-x

> 
> At 02:23 PM 1/12/04 -0500, you wrote:
> >At 07:14 PM 1/12/04 +0100, you wrote:
> >>On Mon, 2004-01-12 at 20:05, Yu Sun (Denis) wrote:
> >> > Dear Gmx-usrs,
> >> >
> >> > We want to run mdrun  (sequential verison) job on the specific node of our
> >> > cluster.
> >> > When I run mdrun as follows:
> >> >
> >> > mpprun -map 1 mdrun  <options ..>
> >> >
> >> > it gives me the following error msg:
> >> >
> >> >     error while loading shared libraries libmd.so.2
> >> >     cannot open shared object file: No such file or directory
> >> >
> >> > But when I run directly without mpprun
> >> > mdrun <options ...>
> >> > There are no problems.
> >>Is this also on the Beowulf node? Most likely your gromacs installation
> >>is not NFS mounted in the cluster, or you should source GMXRC or you
> >>should compile statically.
> >
> >This is on the cluster head node. I can know it  by using beostatus
> >
> >
> >
> >> >
> >> > For other programs, I can use mpprun  to assign job to specific node
> >> > without problem.
> >> >
> >> > Do you have any ideas?
> >> >
> >> > Thank you !
> >> >
> >> >
> >> >
> >> > Yu Sun  (Denis)
> >> > Postdoc
> >> > Department of Bioengineering
> >> > Clemson, SC 29631
> >> > Tel. (864)656-1352
> >> > email: yus at clemson.edu
> >> >
> >> > _______________________________________________
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> >>--
> >>David.
> >>________________________________________________________________________
> >>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> >>Dept. of Cell and Molecular Biology, Uppsala University.
> >>Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >>phone:  46 18 471 4205          fax: 46 18 511 755
> >>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >>_______________________________________________
> >>gmx-users mailing list
> >>gmx-users at gromacs.org
> >>http://www.gromacs.org/mailman/listinfo/gmx-users
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> >
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the www 
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> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++